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BioMed Research International
Volume 2013 (2013), Article ID 731516, 7 pages
http://dx.doi.org/10.1155/2013/731516
Review Article

Aptamers: Novel Molecules as Diagnostic Markers in Bacterial and Viral Infections?

1Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Science, University of São Paulo, Avenida Professor Lineu Prestes 1374, 05508-000 São Paulo, SP, Brazil
2Department of Pediatric Cardiology, Heart Centre Leipzig, Translational Centre for Regenerative Medicine (TRM), University of Leipzig, Strümpellstraße 39, 04289 Leipzig, Germany
3Department of Biochemistry, Institute of Chemistry, University of São Paulo, Avenida Professor Lineu Prestes 748, 05508-900 São Paulo, SP, Brazil

Received 6 June 2013; Accepted 30 July 2013

Academic Editor: Sudhish Mishra

Copyright © 2013 Flávia M. Zimbres et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. G. Shi, F. Yagyu, Y. Shimizu et al., “Flow cytometric assay using two fluorescent proteins for the function of the internal ribosome entry site of hepatitis C virus,” Cytometry Part A, vol. 79, no. 8, pp. 653–660, 2011. View at Publisher · View at Google Scholar · View at Scopus
  2. F. Gondois-Rey, S. Granjeaud, S. L. T. Kieu, D. Herrera, I. Hirsch, and D. Olive, “Multiparametric cytometry for exploration of complex cellular dynamics,” Cytometry Part A, vol. 81, no. 4, pp. 332–342, 2012. View at Publisher · View at Google Scholar · View at Scopus
  3. J. Pollara, L. Hart, F. Brewer et al., “High-throughput quantitative analysis of HIV-1 and SIV-specific ADCC-mediating antibody responses,” Cytometry Part A, vol. 79, no. 8, pp. 603–612, 2011. View at Publisher · View at Google Scholar · View at Scopus
  4. J. M. Mateos-Pérez, R. Redondo, R. Nava et al., “Comparative evaluation of autofocus algorithms for a real-time system for automatic detection of Mycobacterium tuberculosis,” Cytometry Part A, vol. 81, no. 3, pp. 213–221, 2012. View at Publisher · View at Google Scholar · View at Scopus
  5. M. Ruger, G. Bensch, R. Tungler, and U. Reichl, “A flow cytometric method for viability assessment of Staphylococcus aureus and Burkholderia cepacia in mixed culture,” Cytometry Part A, vol. 81, pp. 1055–1066, 2012.
  6. A. D. Ellington and J. W. Szostak, “In vitro selection of RNA molecules that bind specific ligands,” Nature, vol. 346, no. 6287, pp. 818–822, 1990. View at Publisher · View at Google Scholar · View at Scopus
  7. C. Tuerk and L. Gold, “Systemic evolution of ligands by exponential enrichment: RNA ligands to bacteriophage T4 DNA polymerase,” Science, vol. 249, no. 4968, pp. 505–510, 1990. View at Scopus
  8. H. Ulrich, A. H. B. Martins, and J. B. Pesquero, “RNA and DNA aptamers in cytomics analysis,” Current Protocols in Cytometry, vol. 7, pp. 1–39, 2005. View at Scopus
  9. H. Ulrich, A. H. B. Martins, and J. B. Pesquero, “RNA and DNA aptamers in cytomics analysis,” Cytometry Part A, vol. 59, no. 2, pp. 220–231, 2004. View at Scopus
  10. K. Harada and A. D. Frankel, “Identification of two novel arginine binding DNAs,” The EMBO Journal, vol. 14, no. 23, pp. 5798–5811, 1995. View at Scopus
  11. A. S. Davydova, M. A. Vorobjeva, and A. G. Venyaminova, “Escort aptamers: new tools for the targeted delivery of therapeutics into cells,” Acta Naturae, vol. 3, pp. 12–29, 2011.
  12. E. W. M. Ng, D. T. Shima, P. Calias, E. T. Cunningham Jr., D. R. Guyer, and A. P. Adamis, “Pegaptanib, a targeted anti-VEGF aptamer for ocular vascular disease,” Nature Reviews Drug Discovery, vol. 5, no. 2, pp. 123–132, 2006. View at Publisher · View at Google Scholar · View at Scopus
  13. A. A. Nery, C. Wrenger, and H. Ulrich, “Recognition of biomarkers and cell-specific molecular signatures: aptamers as capture agents,” Journal of Separation Science, vol. 32, no. 10, pp. 1523–1530, 2009. View at Publisher · View at Google Scholar · View at Scopus
  14. M. B. Murphy, S. T. Fuller, P. M. Richardson, and S. A. Doyle, “An improved method for the in vitro evolution of aptamers and applications in protein detection and purification,” Nucleic Acids Research, vol. 31, no. 18, p. e110, 2003. View at Scopus
  15. J.-N. Rybak, S. B. Scheurer, D. Neri, and G. Elia, “Purification of biotinylated proteins on streptavidin resin: a protocol for quantitative elution,” Proteomics, vol. 4, no. 8, pp. 2296–2299, 2004. View at Publisher · View at Google Scholar · View at Scopus
  16. H. Ulrich and C. Wrenger, “Disease-specific biomarker discovery by aptamers,” Cytometry Part A, vol. 75, no. 9, pp. 727–733, 2009. View at Publisher · View at Google Scholar · View at Scopus
  17. M. Famulok, G. Mayer, and M. Blind, “Nucleic acid aptamers—from selection in vitro to applications in vivo,” Accounts of Chemical Research, vol. 33, no. 9, pp. 591–599, 2000. View at Publisher · View at Google Scholar · View at Scopus
  18. S. Tombelli, M. Minunni, and M. Mascini, “Analytical applications of aptamers,” Biosensors and Bioelectronics, vol. 20, no. 12, pp. 2424–2434, 2005. View at Publisher · View at Google Scholar · View at Scopus
  19. R. Conrad and A. D. Ellington, “Detecting immobilized protein kinase C isozymes with RNA aptamers,” Analytical Biochemistry, vol. 242, no. 2, pp. 261–265, 1996. View at Publisher · View at Google Scholar · View at Scopus
  20. S. Sekiya, F. Nishikawa, K. Noda, P. K. Kumar, T. Yokoyama, and S. Nishikawa, “In vitro selection of RNA aptamers against cellular and abnormal isoform of mouse prion protein,” Nucleic Acids Symposium Series, no. 49, pp. 361–362, 2005. View at Scopus
  21. A. R. Renslo and J. H. McKerrow, “Drug discovery and development for neglected parasitic diseases,” Nature Chemical Biology, vol. 2, no. 12, pp. 701–710, 2006. View at Publisher · View at Google Scholar · View at Scopus
  22. B. Bloom and P. Fine, “The BCG experience: implications for future vaccines against tuberculosis,” in Tuberculosis: Pathogenesis, Protection and Control, B. R. Bloom, Ed., pp. 531–557, ASM Press, Washington, DC, USA, 1994.
  23. F. Chen, J. Zhou, F. Luo, A.-B. Mohammed, and X.-L. Zhang, “Aptamer from whole-bacterium SELEX as new therapeutic reagent against virulent Mycobacterium tuberculosis,” Biochemical and Biophysical Research Communications, vol. 357, no. 3, pp. 743–748, 2007. View at Publisher · View at Google Scholar · View at Scopus
  24. F. Chen, Y. Hu, D. Li, H. Chen, and X.-L. Zhang, “CS-SELEX generates high-affinity ssDNA aptamers as molecular probes for hepatitis C virus envelope glycoprotein E2,” PLoS ONE, vol. 4, no. 12, Article ID e8142, 2009. View at Publisher · View at Google Scholar · View at Scopus
  25. R. Joshi, H. Janagama, H. P. Dwivedi et al., “Selection, characterization, and application of DNA aptamers for the capture and detection of Salmonella enterica serovars,” Molecular and Cellular Probes, vol. 23, no. 1, pp. 20–28, 2009. View at Publisher · View at Google Scholar · View at Scopus
  26. M. Zuker, “Mfold web server for nucleic acid folding and hybridization prediction,” Nucleic Acids Research, vol. 31, no. 13, pp. 3406–3415, 2003. View at Publisher · View at Google Scholar · View at Scopus
  27. A. Gupta, J. Fontana, C. Crowe et al., “Emergence of multidrug-resistant Salmonella enterica serotype Newport infections resistant to expanded-spectrum cephalosporins in the United States,” Journal of Infectious Diseases, vol. 188, no. 11, pp. 1707–1716, 2003. View at Publisher · View at Google Scholar · View at Scopus
  28. S. J. Wells, P. J. Fedorka-Cray, D. A. Dargatz, K. Ferris, and A. Green, “Fecal shedding of Salmonella spp. by dairy cows on farm and at cull cow markets,” Journal of Food Protection, vol. 64, no. 1, pp. 3–11, 2001. View at Scopus
  29. B. Malorny and J. Hoorfar, “Toward standardization of diagnostic PCR testing of fecal samples: lessons from the detection of salmonellae in pigs,” Journal of Clinical Microbiology, vol. 43, no. 7, pp. 3033–3037, 2005. View at Publisher · View at Google Scholar · View at Scopus
  30. K. T. Carli, A. Eyigor, and V. Caner, “Prevalence of Salmonella serovars in chickens in Turkey,” Journal of Food Protection, vol. 64, no. 11, pp. 1832–1835, 2001. View at Scopus
  31. R. Nayak, P. B. Kenney, J. Keswani, and C. Ritz, “Isolation and characterisation of Salmonella in a turkey production facility,” British Poultry Science, vol. 44, no. 2, pp. 192–202, 2003. View at Publisher · View at Google Scholar · View at Scopus
  32. Q. Pan, X.-L. Zhang, H.-Y. Wu et al., “Aptamers that preferentially bind type IVB pili and inhibit human monocytic-cell invasion by Salmonella enterica serovar typhi,” Antimicrobial Agents and Chemotherapy, vol. 49, no. 10, pp. 4052–4060, 2005. View at Publisher · View at Google Scholar · View at Scopus
  33. X. Cao, S. Li, L. Chen et al., “Combining use of a panel of ssDNA aptamers in the detection of Staphylococcus aureus,” Nucleic Acids Research, vol. 37, no. 14, pp. 4621–4628, 2009. View at Publisher · View at Google Scholar · View at Scopus
  34. R. Wang, J. Zhao, T. Jiang, et al., “Selection and characterization of DNA aptamers for use in detection of avian influenza virus H5N1,” Journal of Virological Methods, vol. 189, pp. 362–369, 2013. View at Publisher · View at Google Scholar
  35. H. R. Liang, Q. Liu, X. X. Zheng, et al., “Aptamers targeting rabies virus-infected cells inhibit viral replication both in vitro and in vivo,” Virus Research, vol. 173, no. 2, pp. 398–403, 2013. View at Publisher · View at Google Scholar
  36. C. P. Neff, J. Zhou, L. Remling et al., “An aptamer-siRNA chimera suppresses HIV-1 viral loads and protects from helper CD4+ T cell decline in humanized mice,” Science Translational Medicine, vol. 3, no. 66, Article ID 66ra6, 2011. View at Publisher · View at Google Scholar · View at Scopus
  37. T. S. Fisher, P. Joshi, and V. R. Prasad, “Mutations that confer resistance to template-analog inhibitors of human immunodeficiency virus (HIV) type 1 reverse transcriptase lead to severe defects in HIV replication,” Journal of Virology, vol. 76, no. 8, pp. 4068–4072, 2002. View at Publisher · View at Google Scholar · View at Scopus
  38. D. M. Held, J. D. Kissel, D. Saran, D. Michalowski, and D. H. Burke, “Differential susceptibility of HIV-1 reverse transcriptase to inhibition by RNA aptamers in enzymatic reactions monitoring specific steps during genome replication,” Journal of Biological Chemistry, vol. 281, no. 35, pp. 25712–25722, 2006. View at Publisher · View at Google Scholar · View at Scopus
  39. D. H. Burke, L. Scates, K. Andrews, and L. Gold, “Bent pseudoknots and novel RNA inhibitors of type 1 human immunodeficiency virus (HIV-1) reverse transcriptase,” Journal of Molecular Biology, vol. 264, no. 4, pp. 650–666, 1996. View at Publisher · View at Google Scholar · View at Scopus
  40. P. Joshi and V. R. Prasad, “Potent inhibition of human immunodeficiency virus type 1 replication by template analog reverse transcriptase inhibitors derived by SELEX (systematic evolution of ligands by exponential enrichment),” Journal of Virology, vol. 76, no. 13, pp. 6545–6557, 2002. View at Publisher · View at Google Scholar · View at Scopus
  41. C. Tuerk, S. MacDougal, and L. Gold, “RNA pseudoknots that inhibit human immunodeficiency virus type 1 reverse transcriptase,” Proceedings of the National Academy of Sciences of the United States of America, vol. 89, no. 15, pp. 6988–6992, 1992. View at Publisher · View at Google Scholar · View at Scopus
  42. F. D. Lowy, “Medical progress: Staphylococcus aureus infections,” The New England Journal of Medicine, vol. 339, no. 8, pp. 520–532, 1998. View at Publisher · View at Google Scholar · View at Scopus
  43. N. M. Qtaishat, H. A. Gussin, and D. R. Pepperberg, “Cysteine-terminated B-domain of Staphylococcus aureus protein A as a scaffold for targeting GABA(A) receptors,” Analytical Biochemistry, vol. 432, pp. 49–57, 2013.
  44. D. Beier and R. Gross, “Regulation of bacterial virulence by two-component systems,” Current Opinion in Microbiology, vol. 9, no. 2, pp. 143–152, 2006. View at Publisher · View at Google Scholar · View at Scopus
  45. S. Bronner, H. Monteil, and G. Prévost, “Regulation of virulence determinants in Staphylococcus aureus: complexity and applications,” FEMS Microbiology Reviews, vol. 28, no. 2, pp. 183–200, 2004. View at Publisher · View at Google Scholar · View at Scopus
  46. A. Loughman, T. Sweeney, F. M. Keane, G. Pietrocola, P. Speziale, and T. J. Foster, “Sequence diversity in the A domain of Staphylococcus aureus fibronectin-binding protein A,” BMC Microbiology, vol. 8, article 74, 2008. View at Publisher · View at Google Scholar · View at Scopus
  47. M. W. van der Woude and A. J. Bäumler, “Phase and antigenic variation in bacteria,” Clinical Microbiology Reviews, vol. 17, no. 3, pp. 581–611, 2004. View at Publisher · View at Google Scholar · View at Scopus
  48. P. Bellecave and D. Moradpour, “A fresh look at interferon-alpha signaling and treatment outcomes in chronic hepatitis C,” Hepatology, vol. 48, pp. 1330–1333, 2008.
  49. N. Boyer and P. Marcellin, “Pathogenesis, diagnosis and management of hepatitis C,” Journal of Hepatology, vol. 32, no. 1, pp. 98–112, 2000. View at Scopus
  50. C. H. Liu, C. J. Liu, C. L. Lin, et al., “Pegylated interferon-alpha-2a plus ribavirin for treatment-naive Asian patients with hepatitis C virus genotype 1 infection: a multicenter, randomized controlled trial,” Clinical Infectious Diseases, vol. 47, pp. 1260–1269, 2008. View at Publisher · View at Google Scholar
  51. M. Sarasin-Filipowicz, E. J. Oakeley, F. H. T. Duong et al., “Interferon signaling and treatment outcome in chronic hepatitis C,” Proceedings of the National Academy of Sciences of the United States of America, vol. 105, no. 19, pp. 7034–7039, 2008. View at Publisher · View at Google Scholar · View at Scopus
  52. B. A. Sullenger, H. F. Gallardo, G. E. Ungers, and E. Gilboa, “Overexpression of TAR sequences renders cells resistant to human immunodeficiency virus replication,” Cell, vol. 63, no. 3, pp. 601–608, 1990. View at Publisher · View at Google Scholar · View at Scopus
  53. A. K. Dey, M. Khati, M. Tang, R. Wyatt, S. M. Lea, and W. James, “An aptamer that neutralizes R5 strains of human immunodeficiency virus type 1 blocks gp120-CCR5 interaction,” Journal of Virology, vol. 79, no. 21, pp. 13806–13810, 2005. View at Publisher · View at Google Scholar · View at Scopus
  54. M. Khati, M. Schüman, J. Ibrahim, Q. Sattentau, S. Gordon, and W. James, “Neutralization of infectivity of diverse R5 clinical isolates of human immunodeficiency virus type 1 by gp120-binding 2F-RNA aptamers,” Journal of Virology, vol. 77, no. 23, pp. 12692–12698, 2003. View at Publisher · View at Google Scholar · View at Scopus
  55. J. Jaeger, T. Restle, and T. A. Steitz, “The structure of HIV-1 reverse transcriptase complexed with an RNA pseudoknot inhibitor,” The EMBO Journal, vol. 17, no. 15, pp. 4535–4542, 1998. View at Publisher · View at Google Scholar · View at Scopus
  56. L. Chaloin, M. J. Lehmann, G. Sczakiel, and T. Restle, “Endogenous expression of a high-affinity pseudoknot RNA aptamer suppresses replication of HIV-1,” Nucleic Acids Research, vol. 30, no. 18, pp. 4001–4008, 2002. View at Scopus
  57. M. J. Lange, T. K. Sharma, A. S. Whatley, et al., “Robust suppression of HIV replication by intracellularly expressed reverse transcriptase aptamers is independent of ribozyme processing,” Molecular Therapy, vol. 20, pp. 2304–2314, 2012. View at Publisher · View at Google Scholar
  58. H. Ulrich and C. Wrenger, “Identification of aptamers as specific binders and modulators of cell-surface receptor activity,” Methods in Molecular Biology, vol. 986, pp. 17–39, 2013.
  59. N. Ferrara, H.-P. Gerber, and J. LeCouter, “The biology of VEGF and its receptors,” Nature Medicine, vol. 9, no. 6, pp. 669–676, 2003. View at Publisher · View at Google Scholar · View at Scopus
  60. J. Ruckman, L. S. Green, J. Beeson et al., “2-fluoropyrimidine RNA-based aptamers to the 165-amino acid form of vascular endothelial growth factor (VEGF165): inhibition of receptor binding and VEGF-induced vascular permeability through interactions requiring the exon 7-encoded domain,” Journal of Biological Chemistry, vol. 273, no. 32, pp. 20556–20567, 1998. View at Publisher · View at Google Scholar · View at Scopus